But Burton's Batman was meant to adapt the early comics Batman, and that was a time when he DID kill.

You can't expect every (or any, really) film adaptation to be faithful to every aspect from every time period of a characters history. Even Nolan's movies ignore and contradict large portions of Batman's comic history. And that's okay, because Nolan's intention was adapting Batman from 1970s-1990s. Just like Burton's intention was to adapt the Batman of the early '40s.